def calc_axial_plane(self, other_center):
"""
(Residue, Point) -> Plane
given another point, calculate the axial plane based on self.center
"""
vec = self.get_center() - other_center
return get_perp_plane(vec, self.center)
def get_atb_res_spat_dist(self):
"""
(CylinderSpatialDistritbution) -> Counter
return the count of antibody residues that fall in the respective rings in the cylinder
"""
if not hasattr(self, "atb_res_spat_dist"):
plane = get_perp_plane(self.get_atb_center() - self.get_paratope_center(), self.get_paratope_center())
cylinder = self.make_cylinder(self.get_paratope_center(), plane)
self.atb_res_cnt_spat_dist = cylinder.get_count_distribution(self.atb.residues)
self.atb_res_spat_dist = cylinder.get_residue_distribution(self.atb.residues)
return self.atb_res_cnt_spat_dist, self.atb_res_spat_dist
def get_tri_spat_dist(self):
"""
(CylinderSpatialDistritbution) -> Counter
return the count of antigen residue triangle that fall in the respective rings in the cylinder
"""
if not hasattr(self, "tri_spat_dist"):
plane = get_perp_plane(self.get_atg_center() - self.get_epitope_center(), self.get_epitope_center())
cylinder = self.make_cylinder(self.get_epitope_center(), plane)
self.tri_cnt_spat_dist = cylinder.get_count_distribution(self.get_triangles())
self.tri_spat_dist = cylinder.get_residue_distribution(self.get_triangles())
return self.tri_cnt_spat_dist, self.tri_spat_dist
def gcb_gen_cylinder(self):
"""
Generate the cylinder geometry data(center and axial plane)
Point: middle point of the line segment between `paratope geometric center` and `epitope geometric center`
Plane: the plane 1, which is perpendicular to the above line segment and 2, in which the `Point` lies in
"""
from ve.fp.geom import Vector, get_perp_plane
#the line between epitope center and paratope center
line = Vector(self.get_epi_center() - self.get_para_center())
#get the paratope and epitope center as the cylinder center
self.cylinder_center = self.get_paraepi_center()
#get the axial plane
self.axial_plane = get_perp_plane(line, self.cylinder_center)
def get_axial_plane(self):
"""get the axial plane(中轴面)of the compelx"""
if hasattr(self, "axial_plane"):
return self.axial_plane
# first set the epitope and paratope center
# vector between epitope center and paratope center
norm_vec = self.get_epi_center() - self.get_para_center()
# the point that the plane passes through
point = self.get_paraepi_center()
# calculate the axial plane based on the point and the vector
from ve.fp.geom import get_perp_plane
plane = get_perp_plane(norm_vec, point)
# set it
self.axial_plane = plane
return self.axial_plane